16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

Acknowledgements The authors acknowledge the assistance of Grietje Holtrop (RINH-BioSS) with the statistical analysis of the data and the Wellcome Trust Sanger Institute’s 454 pyrosequencing team for generating 16S rRNA gene data. AWW, PS and JP received core funding support from the Wellcome Trust [grant number 098051]. AWW, JCM, HJF and KPS are funded by the Scottish Government (SG-RESAS).Peer reviewedPublisher PD

Special issue : The Human Intestinal Microbiota

Peer reviewedPublisher PD

Measured and modeled energy balance parameters to evaluate the environmental conditions of reforestation

In order to develop three models for use in quantifying the environmental conditions of reforestation, extensive measurements required for energy balance calculations were taken for a reforestation site in southwest Oregon. The models are used to decrease the number of measurements required to properly evaluate the potential for heat or moisture stress at a specific reforestation site. The first model, a modification of the Priestley-Taylor evaporation equation, is calibrated to allow prediction of actual evaporation from net radiation and soil heat flux under nonsaturated, soil water limited conditions. By combining Bowen ratio measurements of evaporation and soil water content, an equation was developed to calculate a modified Priestley-Taylor coefficient, α', as a function of soil water content. When the soil is near field capacity α' is ≈ 0.85. Under drier soil conditions, the decrease in α is well described by an exponential equation. The soil water content did not become limiting to evapotranspiration until 60 percent of the available water was used. The second model uses the inverse solution to the soil heat flow equation to determine soil thermal conductivity for layered, heterogeneous soils. The results of the model indicate that soil thermal properties could be adequately modeled by separating the soil into four physical layers to account for the variability in soil water content, bulk density and rock fragment content. The four layer soil model could predict temperatures within 0.3°C and soil heat flux within 0.006 MJ /m² /day. The third model predicts solar radiation. The model incorporates thorough treatment of all components of radiation, (Rayleigh scatter, aerosol scatter, multiple reflected, ground reflected and direct beam radiation) yet only requires the basic site measurements of slope, aspect, latitude, longitude, elevation, and ground albedo. These data are combined with a simple estimate of turbidity (either from a local weather station or literature values) and literature values for atmospheric content of ozone and water vapor to provide a good estimate of potential solar radiation. The model also considers the anisotropic distribution of diffuse radiation and the strong influence that blocking ridges have on total diffuse radiation as well as direct beam. The model was tested using data collected from six sites with different atmospheric conditions and topographic settings

Incorporating anthropogenic influences into fire probability models : effects of human activity and climate change on fire activity in California

The costly interactions between humans and wildfires throughout California demonstrate the need to understand the relationships between them, especially in the face of a changing climate and expanding human communities. Although a number of statistical and process-based wildfire models exist for California, there is enormous uncertainty about the location and number of future fires, with previously published estimates of increases ranging from nine to fifty-three percent by the end of the century. Our goal is to assess the role of climate and anthropogenic influences on the state's fire regimes from 1975 to 2050. We develop an empirical model that integrates estimates of biophysical indicators relevant to plant communities and anthropogenic influences at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of explanatory power in the model. We also find that the total area burned is likely to increase, with burned area expected to increase by 2.2 and 5.0 percent by 2050 under climatic bookends (PCM and GFDL climate models, respectively). Our two climate models show considerable agreement, but due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid inland deserts and coastal areas of the south. Given the strength of human-related variables in some regions, however, it is clear that comprehensive projections of future fire activity should include both anthropogenic and biophysical influences. Previous findings of substantially increased numbers of fires and burned area for California may be tied to omitted variable bias from the exclusion of human influences. The omission of anthropogenic variables in our model would overstate the importance of climatic ones by at least 24%. As such, the failure to include anthropogenic effects in many models likely overstates the response of wildfire to climatic change

A role for glycosaminoglycans in the development of collagen fibrils

AbstractExtensive data on the glycosaminoglycan (GAG) composition and the collagen fibril diameter distribution have been collected for a diverse range of connective tissues. It is shown that tissues with the smallest diameter collagen fibrils (mass-average diameter < 60 nm) have high concentrations of hyaluronic acid and that tissues with the largest diameter collagen fibrils (mass-average diameter ∼200 nm) have high concentrations of dermatan sulphate. It is suggested that the lateral growth of fibrils beyond a diameter of about 60 nm is inhibited by the presence of an excess of hyaluronic acid but that this inhibitory effect may be removed by an increasing concentration of chondroitin sulphate and/or dermatan sulphate. It is also postulated that high concentrations of chondroitin sulphate will inhibit fibril growth beyond a mass-average diameter of ∼150 nm. Such an inhibition may in turn be removed by an increasing concentration of dermatan sulphate such that it becomes the dominant GAG present in the tissue

Neoliberal Redistributive Policy: The U.S. Net Social Wage in the 21st Century

In this paper, I examine the trends of fiscal transfers between the state and workers during 1959 - 2012 to understand the net impact of redistributive policy in the United States. This paper presents original net social wage data from and analysis based on the replication and extension of Shaikh and Tonak (2002). The paper investigates the appearance of a post-2001 variation in the net social wage data. The positive net social wage in the 21st century is the result of a combination of factors including the growth of income support, healthcare inflation, neoliberal tax reforms, and macroeconomic instability. Growing economic inequality does not appear to alter the results of the net social wage methodology

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid

This article is protected by copyright. All rights reserved. Acknowledgements: The authors acknowledge support from the Scottish Government Food Land and People programme (RESAS). We would like to thank Lorraine Scobbie and Gary Duncan for technical support. Funding for JP, AWW and 454 pyrosequencing was provided by the Wellcome Trust (grant number 098051).Peer reviewedPublisher PD

Influence of deterministic geologic trends on spatial variability of hydrologic properties in volcanic tuff

Hydrologic properties have been measured on outcrop samples taken from a detailed, two-dimension grid covering a 1.4 km outcrop exposure of the 10-m thick non-welded-to-welded, shardy base microstratigraphic unit of the Tiva Canyon Member of the Miocene Paintbrush Tuff at Yucca Mountain, Nevada. These data allow quantification of spatial trends in rock matrix properties that exist in this important hydrologic unit. Geologic investigation, combined with statistical and geostatistical analyses of the numerical data, indicates that spatial variability of matrix properties is related to deterministic geologic processes that operated throughout the region. Linear vertical trends in hydrologic properties are strongly developed in the shardy base microstratigraphic unit, and they are more accurately modeled using the concept of a thickness-normalized stratigraphic elevation within the unit, rather than absolute elevation. Hydrologic properties appear to be correlated over distances of 0.25 to 0.3 of the unit thickness after removing the deterministic vertical trend. The use of stratigraphic elevation allows scaling of identified trends by unit thickness which may be of particular importance in a basal, topography-blanketing unit such as this one. Horizontal changes in hydrologic properties do not appear to form obvious trends within the limited lateral geographic extent of the ash-flow environment that was examined. Matrix properties appear to be correlated horizontally over distances between 100 and 400 m. The existence and quantitative description of these trends and patterns of vertical spatial continuity should increase confidence in models of hydrologic properties and groundwater flow in this area that may be constructed to support the design of a potential high-level nuclear waste repository at Yucca Mountain

A preliminary characterization of the spatial variability of precipitation at Yucca Mountain, Nevada

Isohyetal maps of precipitation and numerical models for simulating precipitation are needed to characterize natural infiltration at Yucca Mountain, Nevada. The objective of this study was to characterize the spatial variability of precipitation within the domain of the natural catchments overlying the potential repository, and to define preliminary geostatistical models based on differences in storm type for the numerical simulation of precipitation